The involvement of chromatin structure in modulating DNA functions such a transcription, replication, recombination and repair has become increasingly apparent. We have shown that the placement of a nucleosome on a replication initiation site severely compromises replication function of the element. We have also shown that the MATalpha2p repressor positions a nucleosome in the STE6 gene adjacent to the alpha2 operator in a process that requires the histone H4 N-terminal tail. Although this nucleosome covers a downstream TATA box, shifting the TATA box to a position between two nucleosomes does not allow gene expression, suggesting that in this context transcriptional repression functions at an organizational level above the single nucleosome, namely a chromatin domain. We have shown that MATalpha2p organizes a unique gene-length domain comprised of a dinucleosome structural repeat with alternating short and long internucleosomal linkers. The disruption of other genes required for MATalpha2p-mediated repression causes disruption of this domain, event after reduction of the transcriptional activity of the derepressed gene to a fraction of the wildtype level, demonstrating the structural involvement of other non-histone proteins in the domain can be structurally reproduced on a telomeric yeast plasmid. The domain appears to terminate at a position in the STE6 gene that contains a perfect and several close matches to the ARS consensus sequence (ACS). This ACS region of the STE6 gene acts as a functional replication origin in a yeast plasmid. Any mutation in this region that may interfere with origin recognition complex (ORC) protein binding results in the local disruption of the domain, demonstrating a structural involvement of the ACS region. We show that the polarity of the domain, which is asymmetrically propagate ed from the pseudo-symmetrical alpha2 operator, is not influenced by the direction of replication fork passage or downstream OR binding. In isolation, the alpha2 operator with adjacent proximal sequences organizes flanking nucleosomes symmetrically in a telomeric plasmid. We identified HSP82 as a new member of the Saccharomyces cerevisiae early meiotic gene family and showed that basal expression of this gene is determined by the interaction of a promoter proximal heat shock element (HSE) with a nearby repressor element (URSI). We also identified an additional ancillary repressor element (ARE) that is required for efficient repression, and showed that the depression of basal expression of HSP82 utilizes an URSI-bound factors(s) that is genetically linked with the UME6 gene. We proposed a mechanism of meiotic gene induction that proceeds via two distinct steps where the IM1 gene product antagonizes URS1-mediated repression, followed by the stimulation of an HSE-bound factor by Ime2p, resulting in induction of HSP82.